Helix untwisting and bubble formation in circular DNA
arXiv:1305.4051 · doi:10.1063/1.4807381
Abstract
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.
The Journal of Chemical Physics, vol. 138 (2013), in press
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- Statistical method for A-RNA and B-DNA
- Helical Disruptions in Small Loops of DNA
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